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COM MCM > Week 2 > Flashcards

Week 2 Flashcards

1
Q

RNA structure

A

Single stranded, ribonucleotides, more unstable than DNA, contains U (not T)

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2
Q

rRNA

A

Core of ribosome, catalyzes protein synthesis

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3
Q

tRNA

A

Form adaptors that select/hold onto AAs during protein synthesis

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4
Q

mRNA

A

Short lived, coding RNAs in protein synthesis

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5
Q

snRNA

A

direct splicing of pre-mRNA to mRNA (remove introns)

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6
Q

siRNA

A

Regulate eukaryotic gene expression by degrading select mRNA (typical in lab setting)

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7
Q

miRNA

A

Regulate gene expression by blocking translation of select mRNA (more biologically relevant)

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8
Q

RNA Polymerase I

A

Makes rRNA

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9
Q

RNA Polymerase II

A

Makes mRNA

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10
Q

RNA Polymerase III

A

Makes tRNA

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11
Q

Coding strand of gene

A

Non-template strand identical to RNA sequence produced

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12
Q

Transcription start site

A

+1 position, usually has A or G; basal transcription factors and RNA polymerase bind here

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13
Q

Transcription stop site

A

Contains poly A tail which is clipped off during RNA processing

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14
Q

Transcription unit

A

Linear sequence of DNA from start to stop site

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15
Q

Promoter

A

Sequence upstream of start site where basal transcription factors bind, recruit RNA polymerase
Ex: TATA, CAAT

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16
Q

Enhancer/Silencer

A

Short sequences that influence rate of transcription

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17
Q

General Transcription Factors

A

Initiate transcription, form protein-DNA /protein-protein complexes on promoter; position RNA polymerase, pull apart DNA strands, release RNA polymerase

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18
Q

Initiation of transcription

A
  1. TFIID binds to TATA box, recruits TFIIF/RNA Pol II/TFIIE, TFIIH to form initiation complex
  2. DNA strands separate via TFIIH to expose DNA template strand
  3. Polymerization of short lengths of RNA
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19
Q

TFIID

A

Binds to the TATA box during initiation via TBP subunit

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20
Q

TFIIH

A

Unwinds DNA double helix to expose DNA template during initiation

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21
Q

7-methyl-guanosine cap

A

Modification to the 5’ end of mRNA that protects against degradation, helps bind mRNA to ribosome during translation

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22
Q

Histone acetyl transferase (HAT)

A

Acetylates histones to reduce positive charge, loosen interaction with DNA

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23
Q

Histone deacetylases (HDACs)

A

Remove Acetyl group and reverse HAT action

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24
Q

Elongation of transcription

A

RNA Pol II phosphorylated by TFIIH, polymerase leaves promoter and elongation begins - RNA Pol moves stepwise along DNA and unwinds helix

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25
Q

DNA gyrase

A

Relieves superhelical tension during elongation

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26
Q

Termination of transcription

A

RNA Pol encounters termination signals on DNA template - string of AT nucleotide pairs preceded by 2-fold symmetric DNA sequence

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27
Q

Self complementary hairpin structure of RNA

A

Destabilizes interaction between RNA/RNA Pol

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28
Q

mRNA processing

A

Includes 7-methyl-guanosine cap, splicing, and polyadenylation at 3’ end

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29
Q

How transcription is regulated

A

Several regulatory proteins bind to DNA to control activity (homeodomain, zinc finger, leu zipper HLH proteins)

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30
Q

Relationship of TFs and cancer

A

Mutated genes for transcription factors may lead to oncogenes

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31
Q

FMR1 gene

A

Encodes for protein with neurological function; excess number of CGG repeats leads to suscecptibility of cytosine methylation - gene will be silenced/transcription turned off

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32
Q

Start codon

A

AUG/Met/M

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33
Q

Stop codons

A

UAA/UAG/UGA

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34
Q

Silent mutation

A

Does not change the AA

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35
Q

Missense mutation

A

Changes AA in protein with either no effect on function or vastly different function

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36
Q

Nonsense mutation

A

Codon changes to a STOP codon causing premature chain termination; degradation or truncated version of protein

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37
Q

Frameshift mutation

A

Most serious; one or more nucleotides deleted or inserted into ORF - change in codon sequence/alteration of AA sequence

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38
Q

Anticodon loop of tRNA

A

Set of 3 consecutive nucleotides that pair with complementary codon in mRNA molecule

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39
Q

3’ CCA terminal region

A

Binds amino acid that matches the corresponding codon

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40
Q

Wobble hypothesis

A

tRNAs require accurate base pairing only at the first 2 positions of the codon and can tolerate a mismatch at the 3rd position; explains why alternative codons for an AA only differ in 3rd nucleotide

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41
Q

Aminoacyl tRNAs

A

“Activated” AAs; catalyzed by Aminoacyl synthetase

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42
Q

Transcription Factors (general role)

A

Bind to promoter/enhancer to activate/repress transcription; interact with RNA polymerase II

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43
Q

Hox Genes

A

Repetitive DNA regulators that influence axial development; main regulator of Hox genes = RA

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44
Q

Pax Genes

A

Formation of tissues/organs

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45
Q

Aniridia

A

Eye disorder-absence of iris; mutation in PAX6

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46
Q

Lim Proteins

A

Formation of body segments

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47
Q

Dlx Genes

A

Patterning of outgrowing appendages, jaws, inner ear

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48
Q

Msx Genes

A

Prenatal inhibitor of cell differentiation; postnatal proliferative capacity of tissues

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49
Q

Tbx Genes

A

Mesodermal germ layer development (specifies forelimb and hindlimb)

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50
Q

Basic Helix-Loop-Helix Transcription Factors

A

Regulate myogenesis

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51
Q

FOXP2

A

Associated with disorders of speech/language development; human specific; HLH family

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52
Q

Campomelic dyspasia

A

Mutations near SOX9; effects skeletal, reproductive, respiratory systems (Sox9 = Zn finger family)

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53
Q

WT1 gene

A

Wilms tumor suppressor gene; kidney and gonadal development (Zn finger protein)

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54
Q

Hedgehog proteins

A

Use ligand receptor complex; NOT a TF

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55
Q

Hedgehogs and Wnts

A

protein SIGNALS

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56
Q

Hox, Pax, Msx, Lim,etc

A

Transcriptional regulators/TFs

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57
Q

Wnt signaling

A

Transduced to b-catenin which affects transcription (cancer if not regulated)

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58
Q

RAS

A

Proto-oncogene; if mutated will be perpetually active, occurs in 25% of all cancers

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59
Q

HER2

A

Proto-oncogene; Resulting oncoprotein is NEU observed in some breast cancers

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60
Q

EGF receptor

A

Proto-oncogene; Resulting oncoprotein observed in glioblastoma

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61
Q

N-MYC

A

Proto-oncogene; observed in neuroblastoma

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62
Q

c-MYC

A

Proto-oncogene; Observed in Burkitt lymphoma

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63
Q

ABL

A

Proto-oncogene; observed in CML

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64
Q

p53

A

Tumor suppressor; monitors cell cycle checkpoints; observed in 50% human tumors

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65
Q

RB

A

Tumor suppressor; Regulates G1 phase; observed in retinoblastoma

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66
Q

APC

A

Tumor suppressor; Regulates cell proliferation; observed in FAP (precursor of colon cancer)

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67
Q

DCC

A

Tumor suppressor; Involved in cell proliferation, migration, apoptosis; observed in colon cancer

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68
Q

BRCA1/BRCA2

A

Tumor suppressor; Involved in DNA repair and apoptosis; observed in breast cancer

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69
Q

NF-1

A

Tumor suppressor; involved in GAP formation; observed in neurofibromatosis

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70
Q

Epitope

A

Region of antigen binding to Fab fragment of antibody

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71
Q

Indirect ELISA

A

Ag coated well with specific Ab added, then enzyme-linked Ab added, then substrate converts enzyme to colored product; Color indicates amount of Ab to specific Ag

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72
Q

Sandwich ELISA

A

Ab coated well; Ag binds to Ab; 2nd enzyme linked Ab added and substrate converts to colored product; Color indicates quantity of antigen

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73
Q

PCR

A

Separate DNA strands, anneal primers, synthesize DNA; main purpose if AMPLIFICATION for identification of altered genes or foreign DNA

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74
Q

PCR analysis of Huntington’s

A

Many more repeats seen in PCR vs in healthy individual

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75
Q

STRs

A

Forensic application; varying repetitive regions of DNA sequences that identify individuals

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76
Q

Microarrays

A

Fluorescently marked DNA injected onto chip; scanned, intensity of signal demonstrates gene expression

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77
Q

Pregnancy dating

A

LMP clinically used - fertilization plus 2 weeks

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78
Q

Fertilization

A

Occurs in ampulla (distal 2/3 of fallopian tube); results in completion of 2nd meiotic division, restoration of diploid number of chromosomes, metabolic activation of oocyte, initiation of cleavage

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79
Q

Capacitation

A

Glycoprotein coat and seminal plasma proteins removed from plasma membrane of sperm

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80
Q

Hyaluronidase

A

Enzyme that disperses corona radiata for passage of sperm

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81
Q

Zona reaction

A

block to polyspermy

82
Q

Cleavage

A

Occurs 30 hours after fertilization; increase in cell number with decrease in cell size; morula development

83
Q

Blastocyst

A

Assembled during days 5-7 of development; contains blastocyst cavity, inner cell mass, and trophoblast

84
Q

Trophoblast

A

Releases early pregnancy factor (immunosuppressant), supportive cells that line entire blastocyst

85
Q

Inner cell mass

A

Differentiates into epiblast and hypoblast

86
Q

Cytotrophoblast

A

Contains mitotically active stem cells, form placenta

87
Q

Syncytiotrophoblast

A

Contains proteolytic enzymes, secretes hCG (implantation signal)

88
Q

Epiblast

A

Differentiates into amnion, amnionic cavity, ectoderm (ICM derivative)

89
Q

Hypoblast

A

Differentiates into extraembryonic tissue for signaling (ICM derivative)

90
Q

Extraembryonic somatic mesoderm

A

Lines trophoblast, covers amnion

91
Q

Extraembryonic splanchnic mesoderm

A

Lines the yolk sac

92
Q

Derivatives of extraembryonic mesoderm

A

Connecting stalk, primitive blood, chorion

93
Q

Hydatidiform Mole

A

Abnormal trophoblastic proliferation; complete results from fertilization of empty oocyte, partial results from fertilization of a normal oocyte by 2 sperm
Clinical: vaginal bleeding, pelvic pain, enlarged uterus, morning sickness

94
Q

Choriocarcinomas

A

Malignant tumor developed from hydatidiform mole

95
Q

Ectopic pregnancies

A

Most occur in uterine tubes; diagnosed by ultrasound; s/s cramping and pain; due to smoking, PID

96
Q

Placenta previa

A

Implantation too close to the cervix; key feature: vaginal bleeding beyond 20 weeks gestation; risk of hemorrhage

97
Q

Gastrulation

A

Formation of 3 germ layers (ectoderm, mesoderm, endoderm)

98
Q

Ectoderm derivatives

A

skin, hair, nails, CNS

99
Q

Mesoderm derivatives

A

muscle, bone, blood, heart, connective tissues

100
Q

Endoderm derivatives

A

lungs, GI, bladder

101
Q

Primitive streak

A

Forms in epiblast, contains primitive groove where ectoderm involutes

102
Q

Teratoma

A

May be remnant of primitive streak or inappropriately migrated germ cells; mixture of many tissues; can be sacrococcygeal or oropharyngeal

103
Q

Notochord

A

Extends from primitive node anterior to prechordal plate; serves as template for vertebral column; induces neural plate

104
Q

Chordomas

A

Rare aggressive neoplasms of bone; arise from remnants of notochord

105
Q

Paraxial mesoderm

A

Forms somites (myotome, sclerotome, dermatome)

106
Q

Intermediate mesoderm

A

Forms urogenital system (kidneys, gonads)

107
Q

Lateral plate mesoderm

A

Forms connective tissue (blood, lymph, mesenteries, cardiovascular)

108
Q

Cell cycle stages

A

G1, S, G2, M

109
Q

G1 phase

A

RNA, protein synthesis; cell growth; Restriction and G1 checkpoints

110
Q

S phase

A

DNA replication, histone synthesis, centrosome formed, chromosome duplication

111
Q

G2 phase

A

Prepraration for mitosis, ensuring DNA stability; G2 checkpoint

112
Q

M phase

A

Mitosis; Metaphase checkpoint

113
Q

Restriction point

A

Passage requires growth factor independence; limited growth factors lead to cell cycle arrest in G1 phase

114
Q

G1 checkpoint

A

Corrects DNA damage (chemical modifications) before continuing to S phase

115
Q

G2 checkpoint

A

Verify completeness of complete genomic duplication

116
Q

Metaphase checkpoint

A

Ensures chromosomes are attached to mitotic spindle

117
Q

Cyclin-CDK complex

A

Cause changes in phosphorylation of substrates that regulate cell cycle events (cyclins regulate Cdks)

118
Q

CAK

A

Fully activate Cyclin-Cdk complex

119
Q

WEE1 kinase

A

Phosphorylates roof site of Cyclin-Cdk complex to inactivate it

120
Q

Cdc25 phosphatase

A

De-phosphorylates roof site of Cyclin-Cdk to activate it

121
Q

p27

A

CKI-Physical interaction with Cyclin-Cdk complex inactivates it

122
Q

In which phase does Cyclin D complex with CDKs 4,6?

A

G1

123
Q

In which phase does Cyclin E complex with CDK2?

A

G1-S transition

124
Q

In which phase does Cyclin A complex with CDK2?

A

S

125
Q

In which phase does Cyclin A,B complex with CDK1?

A

Mitosis

126
Q

APC/C

A

Activated by Cdc20; ubiquitination of M-cyclin or S-cyclin so CDK inactivated

127
Q

Extrinsic apoptotic pathway

A

Triggered by external stimuli; involves Fas ligand binding to Fas death receptor, FADD, and intiator caspase 8

128
Q

Intrinsic apoptotic pathway

A

Triggered by internal stimuli; MITOCHONDRIAL dependent; release of cytochrome c from mitochondria leads to Apaf1, apoptosome which causes activation of initiator caspase 9

129
Q

Caspase 3

A

Executioner caspase, can be activated by extrinsic (caspase 8) or intrinsic (caspase 9) pathways

130
Q

BAX (BH123) protein in apoptosis

A

Activated and aggregate to induce release of cytochrome c from mitochondria

131
Q

BCL2 protein in apoptosis

A

Anti-apoptotic protein that inhibits BAX pathways

132
Q

Autosomal dominant disorders

A

Only 1 allele needed for expression; M/F can transfer to M/F; recurrent risk of affected children = 50%; vertical transmission in pedigrees

133
Q

Autosomal recessive disorders

A

2 copies of allele needed to influence phenotype; 25% chance of inheritance; 50% chance of becoming a carrier

134
Q

X-linked recessive disorders

A

Female carriers transmit the gene; no male carriers

135
Q

X-linked dominant disorders

A

RARE; no carriers; Males only transmit to females

136
Q

Reduced penetrance

A

Frequency that a gene manifests itself; suggest multifactorial aspects of disease

137
Q

Variable expressivity

A

Range of phenotypes that vary between individuals with a specici genotype

138
Q

Locus heterogeneity

A

Single disorder/trait/pattern of traits caused by mutations in genes at different chromosomal loci

139
Q

Pleiotropy

A

Single gene produces two or more effects

140
Q

When does crossing over occur

A

Prophase I of meiosis

141
Q

Genomic imprinting

A

Methylated genes are silenced/down regulated; ex: Prader Willi, Angelman syndromes

142
Q

Nondisjunction

A

Homologs fail to properly separate; increases with maternal age

143
Q

Aneuploid

A

Abnormal chromosome number (such as trisomy)

144
Q

Genotype frequency

A

Number of desired genotype divided by total number of genotypes

145
Q

Allele/gene frequency

A

Number of desired alleles divided by total number of alleles present

146
Q

Hardy-Weinberg Principle

A

Determines population frequencies of genotypes;

AA=p2, Aa=2pq, aa=q2; p+q=1

147
Q

Polygenic traits

A

Variation thought to be caused by combined effects of multiple genes

148
Q

Multifactorial traits

A

Environmental factors cause variation in trait

149
Q

Heterochromatin

A

Dark staining, genetically inactive; highly condensed; genes will be silenced if relocated near heterochromatin

150
Q

Euchromatin

A

More loosely packed, lighter stained, transcriptionally active

151
Q

Effect of histone acetylation on DNA

A

Loosens interaction between histones and DNA; neutralizes positive charge and promotes transcription

152
Q

Effect of salt linkages on DNA

A

Neutralize negative charged DNA backbone

153
Q

Effect of histone methylation on DNA

A

Keeps histone/DNA interaction loose and promotes transcription

154
Q

Nucleosomes

A

“Beads on a string” configuration, basic unit of chromosome packing

155
Q

CGH Arrays

A

Detects copy number variation by comparing human DNA on chip to reference DNA strand

156
Q

Asymmetry of DNA replication fork

A

Leading strand synthesized continuously, Lagging strand synthesized in segments

157
Q

DNA Helicase

A

Unwinds DNA via ATP hydrolysis to separate strands

158
Q

Topoisomerase

A

Relieves supercoiling of DNA strand (Type I works on one DNA strand, Type II works on both strands)

159
Q

DNA Polymerase

A

Synthesizes RNA from DNA template and has proofreading capability

160
Q

Single-stranded binding proteins

A

Binds ssDNA that has been separated to stabilize DNA and prevent formation of hairpins

161
Q

DNA Ligase

A

Seals nicks in DNA

162
Q

Spontaneous DNA damage

A

Depurination (whole purine gone), Deamination (C to U); if unrepaired lead to deletion or BP substitution

163
Q

DNA damage due to UV radiation

A

Pyrimidine dimers - stacking of pyrimidines that lead to toxic products

164
Q

Ionizing vs. Non-ionizing DNA damage

A

Ionizing does enough damage to misplace electrons from atoms (due to X-rays, CT scans); Non-ionizing does not (UV radiation)

165
Q

Methylated cytosines

A

Produces T mismatched with G bases; repair is ineffective; associated with inactive genes

166
Q

Direct repair

A

Photolyase repairs pyrimidine dimers

167
Q

Base Excision Repair

A

DNA glycosylase recognizes altered base and catalyzes removal; DNA polymerase adds nucleotide and DNA ligase seals nicks

168
Q

Nucleotide Excision Repair

A

Repairs bulky lesion such as thymine dimers; NER complex scans DNA for distortion, cleaves backbone; helicase pulls away lesion, DNA polymerase and ligase repair gap

169
Q

Xeroderma pigmentosum

A

Severe inherited light sensitivity; due to unrepaired thymine dimers; defective XP proteins in NER complex fail to repair DNA

170
Q

Cockayne’s syndrome

A

Due to defect in transcription coupled repair; RNA polymerase permanently stalled at damaged site

171
Q

Transcription coupled repair

A

RNA polymerase stalls at damaged site and signals repair machinery; specific for strand being transcribed

172
Q

Double stranded break repair

A

Non-homologous end joining brings broken strands together via DNA ligation; some nucleotides lost

173
Q

Mismatch repair

A

Removes distortions in DNA via MER complex, DNA polymerase and ligase

174
Q

Hereditary colon cancer

A

Inherited mutation in MER complex; increased susceptibility-tumor will form if good gene acquires a mutation

175
Q

Acceptor (A) site

A

Where mRNA codon exposed to receive aminoacyl tRNA (except Met)

176
Q

Peptidyl (P) site

A

Where aminoacyl tRNA attached

177
Q

Empty (E) site

A

Location occupied by empty tRNA before exiting ribosome

178
Q

Inititiation (Translation)

A

(Met) Initiator tRNA binds to P site of small SU; interacts with mRNA until it finds AUG; large SU added and translation begins

179
Q

Elongation (Translation)

A

Ribosome extends polypeptide chain by loading aminoacyl tRNA that base pairs with A site codon; elongation factors involved for efficiency/proofreading

180
Q

Termination (Translation)

A

Triggered by stop codon-recognized by release factors; peptide chain released from ribosomal complex; catalyzes water and forms COOH end of polypeptide

181
Q

Streptomycin

A

Binds to 30S subunit to disrupt initiation

182
Q

Shiga toxin

A

Binds to 60S subunit to disrupt elongation

183
Q

Clindamycin/erythromycin

A

Binds to 50s subunit to disrupt translocation of ribosome

184
Q

Tetracyclines

A

Binds to 30S subunit to disrupt elongation

185
Q

Puromycin

A

Can trick the cell into binding because it resembles aminoacylated 3’ end of tyrosyl-tRNA; translation will stop

186
Q

Polysomes

A

Clusters of ribosomes that attach to mRNA and make protein synthesis more efficient

187
Q

Transport signal to mitochondria (cytoplasmic)

A

N-terminal hydrophobic alpha helix

188
Q

Transport signal to nucleus (cytoplasmic)

A

Lys/Arg rich signals (KKKRK)

189
Q

Transport signal to retention in ER (secretory)

A

Lys/Asp/Glu/Leu sequence (KDEL)

190
Q

Transport signal to secretory vesicle (secretory)

A

Trp-rich domain

191
Q

Transport signal to lysosome (secretory)

A

M6P

192
Q

Transport signal to plasma membrane (secretory)

A

N-terminal apolar residues

193
Q

TOM

A

Mitochondrial transporter on outer membrane

194
Q

TIM

A

Mitochondrial transporter on inner membrane

195
Q

Chaperones

A

Protect unfolded proteins during transport (HSP70)

196
Q

SRP

A

Recognizes all particles in secretory pathway; attaches to ribosome and initiates translocation into ER

197
Q

Chaperonins

A

Barrel shaped compartments, catalyze folding of proteins

198
Q

Proteolytic cleavage

A

Converts inactive forms of enzymes to active forms

199
Q

Glycosylation

A

Add sugar to protein; O-glycosidic linkage formed with -OH of Ser or Thr, N-glycosidic linkage formed with Asp

200
Q

Phosphorylation

A

Formation of ester bond between phosphate and OH of AA via Ser/Thr and tyrosine kinase; regulates enzyme and protein activity

201
Q

Disulfide bond formation

A

Form between SH group of 2 Cys in ER lumen

COM MCM (2 decks)

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